diff bamCorrelate.xml @ 18:5ea8782d650c draft

Uploaded

--- a/bamCorrelate.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/bamCorrelate.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.2">
+<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.3">
     <description>correlates pairs of BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamCorrelate</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -39,12 +40,12 @@
             --BED $mode.region_file
         #end if
 
-        ## options available in both modes
-        #if $mode.advancedOpt.showAdvancedOpt == "yes":
+        #### options available in both modes
+        #if str($mode.region.value) != '':
+            --region '$mode.region'
+        #end if
 
-            #if str($mode.advancedOpt.region.value) != '':
-            --region '$mode.advancedOpt.region'
-            #end if
+        #if $mode.advancedOpt.showAdvancedOpt == "yes":
 
             $mode.advancedOpt.doNotExtendPairedEnds
             $mode.advancedOpt.ignoreDuplicates
@@ -149,18 +150,19 @@
    :alt: Heatmap of RNA Polymerase II ChIP-seq
 
 
+You can find more details in the `bamCorrelate wiki`_.
+
+.. _bamCorrelate wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
+
+
 **Output files**:
 
 - diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example
 - data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used
 
 
-
-
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>